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Make static selections of large index groups work.
authorMark Abraham <mark.j.abraham@gmail.com>
Wed, 15 Sep 2021 09:29:55 +0000 (11:29 +0200)
committerMark Abraham <mark.j.abraham@gmail.com>
Wed, 15 Sep 2021 10:03:11 +0000 (12:03 +0200)
The default allocation size is the number of atoms, but this does not
work for large static selections. Such selections might well be used
with gmx distance for listing more pairs of atoms than there are
atoms. Fixed by allocating the needed size.

Fixes #4148

docs/release-notes/2021/2021.4.rst patch | blob | history
src/gromacs/selection/evaluate.cpp patch | blob | history
src/gromacs/trajectoryanalysis/tests/distance.cpp patch | blob | history
src/gromacs/trajectoryanalysis/tests/refdata/DistanceModuleTest_HandlesSelectionFromGroup.xml [new file with mode: 0644] patch | blob
src/gromacs/trajectoryanalysis/tests/refdata/DistanceModuleTest_HandlesSelectionFromLargeGroup.xml [new file with mode: 0644] patch | blob
src/gromacs/trajectoryanalysis/tests/simple.ndx [new file with mode: 0644] patch | blob

diff --git a/docs/release-notes/2021/2021.4.rst b/docs/release-notes/2021/2021.4.rst
index 69a9b7cabe8f7cae306c6821464b093559d8c994..8d44aea03978d6686de7ffc76e984696da8d22f3 100644 (file)
--- a/docs/release-notes/2021/2021.4.rst
+++ b/docs/release-notes/2021/2021.4.rst
@@ -24,6 +24,19 @@ grompp now prints a note again when combining center of mass motion removal and
 
 :issue:`4128`
 
+Static selections of large index groups now work
+""""""""""""""""""""""""""""""""""""""""""""""""
+
+Commands like ``gmx distance -f traj.xtc -n ndx.ndx -select "group
+\"Contacts\""`` only worked if the size of ``Contacts`` was less than
+the number of atoms. This restriction was a bug, and has been fixed so
+that ``Contacts`` make take any size.
+
+Other similar uses of static selections derived from index groups will
+also now work.
+
+:issue:`4148`
+
 Fixes that affect portability
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
diff --git a/src/gromacs/selection/evaluate.cpp b/src/gromacs/selection/evaluate.cpp
index fd2be1443437a43bf7c4dee377c195985ed0b1c8..a6b511a3051164867f0aa0173a9387b312543705 100644 (file)
--- a/src/gromacs/selection/evaluate.cpp
+++ b/src/gromacs/selection/evaluate.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 2009,2010,2011,2012,2013 by the GROMACS development team.
  * Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -522,6 +522,7 @@ void _gmx_sel_evaluate_static(gmx_sel_evaluate_t* /* data */,
 {
     if (sel->flags & SEL_UNSORTED)
     {
+        gmx_ana_index_reserve(sel->v.u.g, sel->u.cgrp.isize);
         // This only works if g contains all the atoms, but that is currently
         // the only supported case.
         gmx_ana_index_copy(sel->v.u.g, &sel->u.cgrp, false);
diff --git a/src/gromacs/trajectoryanalysis/tests/distance.cpp b/src/gromacs/trajectoryanalysis/tests/distance.cpp
index 49b0f8cb6309f1f998bc18d55025740f889f9044..95706b6426f9f46341413791bf1d99c9b4c4cc5b 100644 (file)
--- a/src/gromacs/trajectoryanalysis/tests/distance.cpp
+++ b/src/gromacs/trajectoryanalysis/tests/distance.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2013,2014,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2019,2021, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -90,4 +90,20 @@ TEST_F(DistanceModuleTest, HandlesDynamicSelections)
     runTest(CommandLine(cmdline));
 }
 
+TEST_F(DistanceModuleTest, HandlesSelectionFromGroup)
+{
+    const char* const cmdline[] = { "distance", "-select", "group \"Contacts\"" };
+    setInputFile("-n", "simple.ndx");
+    setTopology("simple.gro");
+    runTest(CommandLine(cmdline));
+}
+
+TEST_F(DistanceModuleTest, HandlesSelectionFromLargeGroup)
+{
+    const char* const cmdline[] = { "distance", "-select", "group \"ManyContacts\"" };
+    setInputFile("-n", "simple.ndx");
+    setTopology("simple.gro");
+    runTest(CommandLine(cmdline));
+}
+
 } // namespace
diff --git a/src/gromacs/trajectoryanalysis/tests/refdata/DistanceModuleTest_HandlesSelectionFromGroup.xml b/src/gromacs/trajectoryanalysis/tests/refdata/DistanceModuleTest_HandlesSelectionFromGroup.xml
new file mode 100644 (file)
index 0000000..7301870
--- /dev/null
+++ b/src/gromacs/trajectoryanalysis/tests/refdata/DistanceModuleTest_HandlesSelectionFromGroup.xml
@@ -0,0 +1,2094 @@
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+  <String Name="CommandLine">distance -select 'group "Contacts"'</String>
+  <OutputData Name="Data">
+    <AnalysisData Name="allstats">
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+        <DataValues>
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diff --git a/src/gromacs/trajectoryanalysis/tests/refdata/DistanceModuleTest_HandlesSelectionFromLargeGroup.xml b/src/gromacs/trajectoryanalysis/tests/refdata/DistanceModuleTest_HandlesSelectionFromLargeGroup.xml
new file mode 100644 (file)
index 0000000..01ed5a1
--- /dev/null
+++ b/src/gromacs/trajectoryanalysis/tests/refdata/DistanceModuleTest_HandlesSelectionFromLargeGroup.xml
@@ -0,0 +1,2270 @@
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+  </OutputData>
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diff --git a/src/gromacs/trajectoryanalysis/tests/simple.ndx b/src/gromacs/trajectoryanalysis/tests/simple.ndx
new file mode 100644 (file)
index 0000000..5f1dde8
--- /dev/null
+++ b/src/gromacs/trajectoryanalysis/tests/simple.ndx
@@ -0,0 +1,37 @@
+[ System ]
+   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15
+[ RNA ]
+   1    2    3    7    8    9   10   11   12
+[ RB ]
+   4    5    6
+[ RD ]
+  13   14   15
+[ Ion ]
+   4    5    6
+[ RB ]
+   4    5    6
+[ RD ]
+  13   14   15
+[ Other ]
+  13   14   15
+[ RB ]
+   4    5    6
+[ RD ]
+  13   14   15
+[ Contacts ]
+   2    3
+   1    2
+[ SuccessiveContacts ]
+   1    2
+   2    3
+[ ManyContacts ]
+   1    2
+   1    6
+   1    8
+   1   10
+   1   11
+  10   12
+   2    3
+   2    6
+   2    7
+   2    9
Local GROMACS mirror with custom stuff